|
| Status |
Public on Feb 02, 2012 |
| Title |
d0_kc_diff_1 |
| Sample type |
SRA |
| |
|
| Source name |
Primary human keratinocytes
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: primary keratinocytes
day of differentiation: d0
|
| Treatment protocol |
See above for differentiation induction cell culture conditions
|
| Growth protocol |
Keratinocytes were grown in Gibco SFM medium in sub-confluent conditions for the d0, progenitor state, and induced to differentiate by plating the cells at confluency and treating the cells with SFM medium + 1.2 mM Ca2+ for 3 or 6 days to induce differentiation.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Illumina PE RNA seq library prep protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Paired end RNAseq
d0_kc_diff_1: Progenitor keratinocytes RNA sequencing paired end 1
d0_kc_diff_2: Progenitor keratinocytes RNA sequencing paired end 2
Progenitor keratinocytes BigWig file aligned to hg18
|
| Data processing |
Reads in each sample were aligned to hg18 using TopHat and reference annotation based transcriptome assembly was performed with Cufflinks. Differential expression analysis was performed with the Cuffdiff module of Cufflinks.
Genome Build:
d0_kc_diff.bw: hg18
|
| |
|
| Submission date |
Feb 01, 2012 |
| Last update date |
Oct 11, 2022 |
| Contact name |
Douglas Porter |
| Organization name |
Stanford
|
| Department |
Dermatology
|
| Lab |
Khavari
|
| Street address |
269 Campus Drive
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE35468 |
Transcriptome profiling of epidermal differentiation |
| GSE58161 |
Suppression of progenitor differentiation requires the long noncoding RNA ANCR |
|
| Relations |
| SRA |
SRX118281 |
| BioSample |
SAMN00779914 |
